I got it, geany should have changed its icon when '$prefix/share/icons' changed. It was not changed because a geany was installed from debian repository, that put geany icons to /usr/share/icons. In that case, geany will read icons from /usr/share/icons firstly, '$prefix/share/icons' were ignored. Deleting geany icons from /usr/share/icons or remove debian_repo's_geany fixed this. As a suggestion, maybe geany should not write icons to /usr/share/icons?
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